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- PDB-9k3q: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex -

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Basic information

Entry
Database: PDB / ID: 9k3q
TitleCryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Components
  • (Light-harvesting protein B-870 ...) x 2
  • (Reaction center protein ...) x 2
  • Photoreaction center protein H
KeywordsPHOTOSYNTHESIS / reaction centre light-harvesting 1
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / metal ion binding / membrane / plasma membrane
Similarity search - Function
Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex ...Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Trans-Geranyl BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / UBIQUINONE-10 / Light-harvesting protein B-870 alpha chain / Light-harvesting protein B-870 beta chain / Reaction center protein L chain / Reaction center protein M chain / Photoreaction center protein H
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLiu, Z.K. / Wang, P. / Liu, L.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Authors: Liu, Z.K. / Wang, P. / Liu, L.N.
History
DepositionOct 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Light-harvesting protein B-870 beta chain
2: Light-harvesting protein B-870 alpha chain
3: Light-harvesting protein B-870 beta chain
4: Light-harvesting protein B-870 alpha chain
5: Light-harvesting protein B-870 beta chain
6: Light-harvesting protein B-870 alpha chain
7: Light-harvesting protein B-870 beta chain
8: Light-harvesting protein B-870 alpha chain
9: Light-harvesting protein B-870 beta chain
A: Light-harvesting protein B-870 alpha chain
D: Light-harvesting protein B-870 alpha chain
E: Light-harvesting protein B-870 alpha chain
F: Light-harvesting protein B-870 alpha chain
G: Light-harvesting protein B-870 alpha chain
H: Photoreaction center protein H
I: Light-harvesting protein B-870 beta chain
J: Light-harvesting protein B-870 alpha chain
K: Light-harvesting protein B-870 beta chain
L: Reaction center protein L chain
M: Reaction center protein M chain
N: Light-harvesting protein B-870 alpha chain
O: Light-harvesting protein B-870 beta chain
Q: Light-harvesting protein B-870 beta chain
R: Light-harvesting protein B-870 alpha chain
S: Light-harvesting protein B-870 beta chain
T: Light-harvesting protein B-870 alpha chain
U: Light-harvesting protein B-870 beta chain
V: Light-harvesting protein B-870 alpha chain
W: Light-harvesting protein B-870 beta chain
X: Light-harvesting protein B-870 alpha chain
Y: Light-harvesting protein B-870 beta chain
Z: Light-harvesting protein B-870 alpha chain
d: Light-harvesting protein B-870 beta chain
m: Light-harvesting protein B-870 beta chain
n: Light-harvesting protein B-870 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,81295
Polymers252,88735
Non-polymers47,92560
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Light-harvesting protein B-870 ... , 2 types, 32 molecules 13579IKOQSUWYdmn2468ADEFGJNRTVXZ

#1: Protein/peptide
Light-harvesting protein B-870 beta chain / Antenna pigment protein beta chain / LH-1


Mass: 5037.832 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: P0C190
#2: Protein/peptide
Light-harvesting protein B-870 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 5308.227 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: P02947

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Protein , 1 types, 1 molecules H

#3: Protein Photoreaction center protein H


Mass: 27745.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: Q7M149

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Reaction center protein ... , 2 types, 2 molecules LM

#4: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30472.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pufL / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: P10717
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 29131.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: Rru_A2974 / Production host: Rhodospirillum rubrum (bacteria) / References: UniProt: Q2RQ26

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Non-polymers , 5 types, 60 molecules

#6: Chemical...
ChemComp-07D / Trans-Geranyl BACTERIOCHLOROPHYLL A


Mass: 901.425 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C55H64MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2
#8: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: reaction center_light harvesting complex 1 from Rhodospirillum rubrum
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97584 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00622452
ELECTRON MICROSCOPYf_angle_d0.86531078
ELECTRON MICROSCOPYf_dihedral_angle_d11.6354991
ELECTRON MICROSCOPYf_chiral_restr0.0382820
ELECTRON MICROSCOPYf_plane_restr0.0064575

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